Ccr5 (C-C motif chemokine receptor 5) - Rat Genome Database

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Gene: Ccr5 (C-C motif chemokine receptor 5) Rattus norvegicus
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Symbol: Ccr5
Name: C-C motif chemokine receptor 5
RGD ID: 620596
Description: Exhibits protein kinase binding activity. Involved in several processes, including nervous system development; positive regulation of cytokine production; and response to bacterium. Localizes to cell surface and endosome. Used to study Alzheimer's disease; plague; and visual epilepsy. Biomarker of several diseases, including artery disease (multiple); diabetes mellitus (multiple); end stage renal disease; orchitis; and uveitis (multiple). Human ortholog(s) of this gene implicated in several diseases, including Kawasaki disease; West Nile fever; autoimmune disease (multiple); berylliosis; and sarcoidosis (multiple). Orthologous to human CCR5 (C-C motif chemokine receptor 5); PARTICIPATES IN interleukin-12 signaling pathway; chemokine mediated signaling pathway; cytokine mediated signaling pathway; INTERACTS WITH 17alpha-ethynylestradiol; 17beta-estradiol; 17beta-estradiol 3-benzoate.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: C-C chemokine receptor type 5; C-C CKR-5; CC-CKR-5; CCR-5; chemokine (C-C motif) receptor 5; chemokine (C-C) receptor 5; Ckr5; Cmkbr5; MIP-1 alpha receptor
RGD Orthologs
Human
Mouse
Bonobo
Dog
Pig
Green Monkey
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.28123,752,423 - 123,757,538 (+)NCBI
Rnor_6.0 Ensembl8133,197,032 - 133,215,614 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.08133,192,398 - 133,215,599 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.08132,362,664 - 132,367,779 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.48128,907,157 - 128,912,272 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.18128,929,594 - 128,932,000 (+)NCBI
Celera8122,847,673 - 122,852,786 (+)NCBICelera
Cytogenetic Map8q32NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
acquired immunodeficiency syndrome  (ISO)
Acute Hepatitis  (ISO)
acute kidney failure  (ISO)
Alcoholic Fatty Liver  (ISO)
allergic contact dermatitis  (IEP)
Alzheimer's disease  (IMP,ISO)
anterior uveitis  (IEP)
Arterial Injury  (IEP)
arteriosclerosis  (ISO)
asthma  (ISO)
atherosclerosis  (ISO)
atopic dermatitis  (ISO)
Behcet's disease  (ISO)
berylliosis  (ISO)
Birth Injuries  (IEP)
Brain Injuries  (IEP)
brain ischemia  (IEP)
breast cancer  (ISO)
cerebral infarction  (ISO)
Chemical and Drug Induced Liver Injury  (ISO)
chlamydia  (ISO)
Chronic Hepatitis C  (ISO)
chronic obstructive pulmonary disease  (ISO)
corneal neovascularization  (ISO)
coronary artery disease  (IEP)
Coronary Disease  (ISO)
Coronavirus infectious disease  (ISO,ISS)
cutaneous leishmaniasis  (ISO)
Diabetic Nephropathies  (ISO)
diabetic retinopathy  (ISO)
dry eye syndrome  (ISO)
end stage renal disease  (IEP)
Experimental Arthritis  (IEP)
Experimental Autoimmune Encephalomyelitis  (IEP)
Experimental Diabetes Mellitus  (IEP)
Experimental Liver Cirrhosis  (ISO)
fallopian tube disease  (ISO)
Fever  (IMP,ISO)
Flaviviridae Infections  (ISO)
gallbladder cancer  (ISO)
glaucoma  (ISO)
Graft vs Host Disease  (ISO)
granulomatosis with polyangiitis  (ISO)
hepatitis B  (ISO)
hepatitis C  (ISO)
Herpes Simplex Encephalitis  (ISO)
herpes simplex virus keratitis  (ISO)
human immunodeficiency virus infectious disease  (ISO)
Human Influenza  (ISO)
Hyperalgesia  (IEP,IMP,ISO)
hypertension  (IEP,ISO)
Hypoxia-Ischemia, Brain  (IEP)
Inflammation  (IEP)
interstitial lung disease  (ISO)
juvenile rheumatoid arthritis  (ISO)
Kawasaki disease  (ISO)
keratoconjunctivitis sicca  (ISO)
leishmaniasis  (ISO)
Liver Injury  (IMP)
Lymphatic Metastasis  (ISO)
Mammary Neoplasms, Experimental  (ISO)
multiple sclerosis  (ISO)
Mycoplasma Infections  (ISO)
Mycoplasma pneumoniae pneumonia  (ISO)
Myocardial Reperfusion Injury  (IEP,ISO)
nephritis  (ISO)
optic neuritis  (ISO)
Oral Lichen Planus  (ISO)
orchitis  (IEP)
ovarian carcinoma  (ISO)
pancreatic cancer  (ISO)
paracoccidioidomycosis  (ISO)
Perennial Allergic Rhinitis  (ISO)
plague  (IAGP)
pleural tuberculosis  (ISO)
pneumonia  (ISO)
posterior uveitis  (ISO)
psoriasis  (ISO)
pulmonary emphysema  (ISO)
pulmonary fibrosis  (ISO)
pulmonary sarcoidosis  (ISO)
pulmonary tuberculosis  (ISO)
respiratory syncytial virus infectious disease  (ISO)
Respirovirus Infections  (ISO)
rheumatoid arthritis  (ISO)
sarcoidosis  (ISO)
Sjogren's syndrome  (ISO)
status epilepticus  (IEP)
syphilis  (ISO)
systemic lupus erythematosus  (ISO)
Transplant Rejection  (IEP)
type 1 diabetes mellitus  (IEP,ISO)
type 1 diabetes mellitus 22  (ISO)
type 2 diabetes mellitus  (IEP,ISO)
Ulcer  (ISO)
urticaria  (ISO)
uveitis  (IEP)
visceral leishmaniasis  (ISO)
visual epilepsy  (IMP)
West Nile fever  (ISO)

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(R)-mevalonic acid  (ISO)
(S)-nicotine  (ISO)
1,3-benzothiazole-2-thiol  (ISO)
1-chloro-2,4-dinitrobenzene  (ISO)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (EXP)
17beta-estradiol 3-benzoate  (EXP)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4,6-trinitrobenzenesulfonic acid  (ISO)
2-naphthylamine  (ISO)
3-chlorophenol  (ISO)
4-amino-2,6-dinitrotoluene  (EXP)
4-hydroxyphenyl retinamide  (ISO)
acetamide  (EXP)
aflatoxin B1  (EXP,ISO)
ammonium chloride  (EXP)
amphetamine  (EXP)
antirheumatic drug  (ISO)
benzalkonium chloride  (ISO)
benzene  (ISO)
benzo[a]pyrene  (ISO)
bis(2-chloroethyl) sulfide  (ISO)
bisphenol A  (EXP)
bisphenol F  (ISO)
bleomycin A2  (ISO)
buta-1,3-diene  (ISO)
carbon nanotube  (ISO)
celecoxib  (ISO)
chloroprene  (ISO)
cisplatin  (ISO)
clofibrate  (ISO)
cocaine  (ISO)
crocidolite asbestos  (ISO)
cyclophosphamide  (ISO)
cyclosporin A  (ISO)
cyproterone acetate  (ISO)
D-penicillamine  (EXP)
dextran sulfate  (ISO)
diclofenac  (ISO)
dioxygen  (ISO)
disulfiram  (ISO)
ethyl methanesulfonate  (ISO)
eugenol  (ISO)
formaldehyde  (ISO)
graphene oxide  (ISO)
indole-3-methanol  (ISO)
isopentenyl diphosphate  (ISO)
ketamine  (EXP)
lipopolysaccharide  (ISO)
maraviroc  (ISO)
mechlorethamine  (EXP)
mercury dichloride  (EXP)
methamphetamine  (EXP)
methyl methanesulfonate  (ISO)
mycotoxin  (ISO)
nickel atom  (ISO)
nicotine  (ISO)
nitric oxide  (ISO)
oxaliplatin  (EXP)
paracetamol  (ISO)
pentachlorophenol  (ISO)
phenobarbital  (ISO)
pirinixic acid  (ISO)
proanthocyanidin  (ISO)
prostaglandin E2  (ISO)
protein kinase inhibitor  (ISO)
reactive oxygen species  (ISO)
resveratrol  (ISO)
SCH 23390  (EXP)
silicon dioxide  (ISO)
simvastatin  (EXP,ISO)
sodium dodecyl sulfate  (ISO)
Soman  (EXP)
staurosporine  (EXP)
testosterone  (EXP)
tetrachloromethane  (ISO)
titanium dioxide  (ISO)
topotecan  (EXP)
tremolite asbestos  (ISO)
trichostatin A  (ISO)
trimellitic anhydride  (ISO)
troglitazone  (ISO)
vinclozolin  (EXP)
wortmannin  (ISO)
zidovudine  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
aging  (IEP)
calcium ion transport  (ISO)
calcium-mediated signaling  (IBA,IEA,ISO)
cell chemotaxis  (IBA)
cell-cell signaling  (IEA,ISO)
cellular response to lipopolysaccharide  (IEA,ISO)
chemokine-mediated signaling pathway  (IEA)
chemotaxis  (IEA)
defense response  (ISO)
defense response to bacterium  (IEP)
fat cell differentiation  (IEP)
forebrain development  (IEP)
G protein-coupled receptor signaling pathway  (IEA,ISO)
immune response  (IBA,IEA)
inflammatory response  (IBA,IEA,IEP)
inflammatory response to antigenic stimulus  (IEP)
leukocyte migration  (TAS)
MAPK cascade  (IEA,ISO)
negative regulation of axon extension  (IMP)
negative regulation of cell migration  (IMP)
negative regulation of macrophage apoptotic process  (IEA,ISO)
negative regulation of neural precursor cell proliferation  (IMP)
neuron death  (IMP)
positive regulation of apoptotic process by virus  (IMP)
positive regulation of cell-cell adhesion  (IMP)
positive regulation of cytosolic calcium ion concentration  (IBA,IMP)
positive regulation of fever generation  (IMP)
positive regulation of gene expression  (IMP)
positive regulation of inflammatory response  (IMP)
positive regulation of interleukin-1 beta production  (IMP)
positive regulation of interleukin-6 production  (IMP)
positive regulation of neuron differentiation  (IMP)
positive regulation of tumor necrosis factor production  (IMP)
release of sequestered calcium ion into cytosol by sarcoplasmic reticulum  (IEA,ISO)
response to cholesterol  (IEA,ISO)
response to ionizing radiation  (IEP)
response to lipopolysaccharide  (IEP)
signaling  (ISO)

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
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Additional References at PubMed
PMID:8631787   PMID:8699119   PMID:9139699   PMID:9655467   PMID:10383387   PMID:10521508   PMID:10528159   PMID:10679098   PMID:11278962   PMID:12032188   PMID:12421915   PMID:16208318  
PMID:16301745   PMID:16841089   PMID:18230715   PMID:18632580   PMID:19008373   PMID:19523456   PMID:21515370   PMID:22353418   PMID:23610400   PMID:23620790   PMID:24086760   PMID:25300256  
PMID:26550961   PMID:26740279   PMID:26983670   PMID:27848062   PMID:31066041   PMID:31574524   PMID:32446198  


Genomics

Comparative Map Data
Ccr5
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.28123,752,423 - 123,757,538 (+)NCBI
Rnor_6.0 Ensembl8133,197,032 - 133,215,614 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.08133,192,398 - 133,215,599 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.08132,362,664 - 132,367,779 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.48128,907,157 - 128,912,272 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.18128,929,594 - 128,932,000 (+)NCBI
Celera8122,847,673 - 122,852,786 (+)NCBICelera
Cytogenetic Map8q32NCBI
CCR5
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl346,370,854 - 46,376,206 (+)EnsemblGRCh38hg38GRCh38
GRCh38346,370,142 - 46,376,206 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37346,411,633 - 46,417,697 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36346,386,637 - 46,392,701 (+)NCBINCBI36hg18NCBI36
Celera346,348,960 - 46,355,024 (+)NCBI
Cytogenetic Map3p21.31NCBI
HuRef346,455,276 - 46,461,340 (+)NCBIHuRef
CHM1_1346,361,630 - 46,367,689 (+)NCBICHM1_1
Ccr5
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm399123,921,557 - 123,934,153 (+)NCBIGRCm39mm39
GRCm39 Ensembl9123,921,580 - 123,947,736 (+)Ensembl
GRCm389124,121,543 - 124,127,183 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl9124,121,543 - 124,147,699 (+)EnsemblGRCm38mm10GRCm38
MGSCv379124,036,282 - 124,041,922 (+)NCBIGRCm37mm9NCBIm37
Celera9124,872,533 - 124,878,180 (-)NCBICelera
Cytogenetic Map9F4NCBI
cM Map975.05NCBI
CCR5
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1347,377,564 - 47,383,625 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl347,380,321 - 47,381,379 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0346,273,096 - 46,278,471 (+)NCBIMhudiblu_PPA_v0panPan3
CCR5
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12042,293,288 - 42,297,952 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2042,294,996 - 42,297,952 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2042,210,909 - 42,213,866 (-)NCBI
ROS_Cfam_1.02042,775,514 - 42,780,183 (-)NCBI
UMICH_Zoey_3.12042,018,434 - 42,021,393 (-)NCBI
UNSW_CanFamBas_1.02042,419,865 - 42,422,824 (-)NCBI
UU_Cfam_GSD_1.02042,700,801 - 42,703,760 (-)NCBI
CCR5
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1329,383,303 - 29,387,902 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11329,382,383 - 29,387,902 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21332,546,545 - 32,551,732 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CCR5
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1227,803,794 - 7,818,112 (+)NCBI

Position Markers
Cmkbr5  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.28123,756,008 - 123,756,165 (+)MAPPER
Rnor_6.08133,214,070 - 133,214,226NCBIRnor6.0
Rnor_5.08132,366,250 - 132,366,406UniSTSRnor5.0
RGSC_v3.48128,910,743 - 128,910,899UniSTSRGSC3.4
Celera8122,851,258 - 122,851,414UniSTS
Cytogenetic Map8q32UniSTS
PMC122923P1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.28123,755,127 - 123,755,373 (+)MAPPER
Rnor_6.08133,213,189 - 133,213,434NCBIRnor6.0
Rnor_5.08132,365,369 - 132,365,614UniSTSRnor5.0
RGSC_v3.48128,909,862 - 128,910,107UniSTSRGSC3.4
Celera8122,850,377 - 122,850,622UniSTS
Cytogenetic Map8q32UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1358893Bp263Blood pressure QTL 2635.01arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)8100873811133307652Rat
1358903Bp252Blood pressure QTL 25270.0001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)8100873811133307652Rat
738011Anxrr9Anxiety related response QTL 96.1exploratory behavior trait (VT:0010471)number of entries into a discrete space in an experimental apparatus (CMO:0000960)8102051964133307652Rat
738014Anxrr15Anxiety related response QTL 153.60.005locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)8104682575133307652Rat
2300182Bmd56Bone mineral density QTL 565.4femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)8104682575133307652Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:18
Count of miRNA genes:18
Interacting mature miRNAs:18
Transcripts:ENSRNOT00000075564
Prediction methods:Miranda, Rnahybrid
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 5 15 8 1 5 6
Low 3 35 52 41 4 41 8 10 66 34 34 5 8
Below cutoff 6 1 2

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000075564   ⟹   ENSRNOP00000066146
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl8133,197,032 - 133,214,257 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000082774   ⟹   ENSRNOP00000073121
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl8133,210,473 - 133,215,614 (+)Ensembl
RefSeq Acc Id: NM_053960   ⟹   NP_446412
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.28123,752,423 - 123,757,538 (+)NCBI
Rnor_6.08133,210,484 - 133,215,599 (+)NCBI
Rnor_5.08132,362,664 - 132,367,779 (+)NCBI
RGSC_v3.48128,907,157 - 128,912,272 (+)RGD
Celera8122,847,673 - 122,852,786 (+)RGD
Sequence:
RefSeq Acc Id: XM_017595419   ⟹   XP_017450908
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.08133,194,146 - 133,214,257 (+)NCBI
Sequence:
RefSeq Acc Id: XR_001839130
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.08133,192,406 - 133,197,171 (+)NCBI
Sequence:
RefSeq Acc Id: XR_001839131
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.08133,192,398 - 133,197,171 (+)NCBI
Sequence:
RefSeq Acc Id: XR_001839132
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.08133,194,123 - 133,197,171 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_446412   ⟸   NM_053960
- UniProtKB: O08556 (UniProtKB/Swiss-Prot),   Q68G28 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017450908   ⟸   XM_017595419
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000073121   ⟸   ENSRNOT00000082774
RefSeq Acc Id: ENSRNOP00000066146   ⟸   ENSRNOT00000075564
Protein Domains
G_PROTEIN_RECEP_F1_2

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

Promoters
RGD ID:13696416
Promoter ID:EPDNEW_R6941
Type:initiation region
Name:Ccr5_1
Description:chemokine (C-C motif) receptor 5
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.08133,210,484 - 133,210,544EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
8 132365535 132365536 C A snv BN/SsNSlc (KyushuU), RCS/Kyo (KyushuU), F344/NSlc (KyushuU), BDIX.Cg-Tal/NemOda (KyushuU), LE/OrlBarth (UDEL), IS/Kyo (KyushuU), LE/Stm (KyushuU), BDIX/NemOda (KyushuU), SDLEF7/Barth (UDEL), LEC/Tj (KyushuU), Crl:SD (UDEL), HWY/Slc (KyushuU), F344/Stm (KyushuU), ZFDM (KyushuU), IS-Tlk/Kyo (KyushuU), NIG-III/Hok (KyushuU), BUF/MNa (KyushuU), ZF (KyushuU)
8 132365926 132365927 C T snv LEC/Tj (KyushuU), F344/Jcl (KyushuU), BDIX/NemOda (KyushuU), DOB/Oda (KyushuU), BDIX.Cg-Tal/NemOda (KyushuU), KFRS3B/Kyo (KyushuU), ZF (KyushuU), F344/Stm (KyushuU), IS-Tlk/Kyo (KyushuU), RCS/Kyo (KyushuU), F344/NSlc (KyushuU), HTX/Kyo (KyushuU), LE/Stm (KyushuU), F344/DuCrlCrlj (KyushuU), NIG-III/Hok (KyushuU), BUF/MNa (KyushuU), IS/Kyo (KyushuU), LE/OrlBarth (UDEL), SS/JrHsdMcwi (MCW), SR/JrHsd (MCW), SBN/Ygl (MCW), FHL/EurMcwi (MCW), FHH/EurMcwi (MCW), SBH/Ygl (MCW), COP/CrCrl (MCW & UW), GH/OmrMcwi (MCW)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
8 133213355 133213356 C A snv WKY/Gcrc (RGD), MHS/Gib (RGD), LL/MavRrrc (RGD), LN/MavRrrc (RGD), CDR, LE/Stm (RGD), BBDP/Wor (RGD), CDS, LEW/NCrlBR (RGD)
8 133213706 133213707 C G snv WKY/Gcrc (RGD), SBN/Ygl (RGD), SBH/Ygl (RGD), BBDP/Wor (RGD)
8 133213709 133213710 A C snv SBH/Ygl (RGD), BBDP/Wor (RGD), SBN/Ygl (RGD), WKY/Gcrc (RGD)
8 133213746 133213747 C T snv WKY/N (MCW), WN/N (MCW), FHL/EurMcwi (RGD), COP/CrCrl (MCW & UW), SR/JrHsd (MCW), BBDP/Wor (RGD), SBN/Ygl (RGD), SBN/Ygl (MCW), CDS, SS/JrHsdMcwi (MCW), FHL/EurMcwi (MCW), Buf/N (MCW), FHH/EurMcwi (MCW), CDR, SBH/Ygl (MCW), GH/OmrMcwi (MCW), WKY/NHsd (RGD), MR/N (MCW), M520/N (MCW), F344/NRrrc (MCW), WKY/Gcrc (RGD), GK/Ox (RGD)
8 133213784 133213785 T A snv LN/MavRrrc (RGD), LEW/Crl (RGD), LL/MavRrrc (RGD), WKY/NCrl (RGD), SR/JrHsd (RGD)
8 133213788 133213789 A T snv LL/MavRrrc (RGD), CDS, SR/JrHsd (RGD), CDR, WKY/NCrl (RGD), LEW/Crl (RGD), LN/MavRrrc (RGD)
8 133213994 133213995 C A snv MNS/Gib (RGD)
8 133213998 133213999 A G snv MNS/Gib (RGD)
8 133214006 133214007 A T snv MNS/Gib (RGD)


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
8 128910419 128910420 C T snv SHR/OlaIpcv (ICL), LCR/2Mco (UMich), SHRSP/Gcrc (MDC), SS/JrHsdMcwi (MDC), BUF/N (KNAW), F344/NRrrc (KNAW), LE/Stm (KNAW), M520/N (KNAW), MR/N (KNAW), WKY/N (KNAW), WN/N (KNAW), SHR/OlaIpcv (KNAW), FHH/EurMcwi (MCW), FHL/EurMcwi (MCW), SR/JrHsd (MCW), SS/JrHsdMcwi (MCW), COP/CrCrl (MCW & UW), GH/OmrMcwi (MCW), BBDP/WorN (ICL), F344/NCrl (ICL), LE/Stm (ICL), FHH/EurMcwi (ICL), FHL/EurMcwi (ICL), GK/Ox (ICL), LEW/Crl (ICL), LEW/NCrl (ICL), LH/MavRrrc (ICL), LL/MavRrrc (ICL), LN/MavRrrc (ICL), MHS/Gib (ICL), MNS/Gib (ICL), SBH/Ygl (ICL), SBN/Ygl (ICL), SHR/OlaIpcv (ICL), SHR/NHsd (ICL), SHRSP/Gcrc (ICL), SR/JrHsd (ICL), SS/Jr (ICL), SS/JrHsdMcwi (ICL), WAG/Rij (ICL), WKY/Gcrc (ICL), WKY/NHsd (ICL), WKY/NCrl (ICL), HCR/1Mco (UMich), LCR/1Mco (UMich), HCR/2Mco (UMich), FHH/EurMcwi (MDC)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:620596 AgrOrtholog
Ensembl Genes ENSRNOG00000049115 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000066146 UniProtKB/TrEMBL
  ENSRNOP00000073121 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000075564 UniProtKB/TrEMBL
  ENSRNOT00000082774 ENTREZGENE, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7109679 IMAGE-MGC_LOAD
InterPro Chemokine_CCR5 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Chemokine_rcpt UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  GPCR_Rhodpsn UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  GPCR_Rhodpsn_7TM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:117029 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGC_CLONE MGC:93260 IMAGE-MGC_LOAD
NCBI Gene 117029 ENTREZGENE
Pfam 7tm_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB CCR5 RGD
PhenoGen Ccr5 PhenoGen
PRINTS CCCHEMOKINER UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CHEMOKINER5 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  GPCRRHODOPSN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE G_PROTEIN_RECEP_F1_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  G_PROTEIN_RECEP_F1_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt CCR5_RAT UniProtKB/Swiss-Prot
  M0R9H7_RAT UniProtKB/TrEMBL
  O08556 ENTREZGENE
  Q68G28 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2018-03-16 Ccr5  C-C motif chemokine receptor 5  Ccr5  chemokine (C-C motif) receptor 5  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-30 Ccr5  chemokine (C-C motif) receptor 5    chemokine (C-C) receptor 5  Name updated 1299863 APPROVED
2004-09-10 Ccr5  chemokine (C-C) receptor 5  Cmkbr5    Symbol and Name updated 1299863 APPROVED
2002-08-07 Cmkbr5  chemokine (C-C) receptor 5      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_regulation phosphorylated by GPCR kinase (GRK)- and protein kinase C (PKC) following RANTES/CCL5 binding to receptor 632395
gene_regulation expression upregulated following bacterial infection 632396
gene_regulation downregulation of receptor is induced by interleukin-1beta 632389